A fifth of Labour MPs defied Jeremy Corbyn’s three-line whip to vote against legislation granting Theresa May the power to trigger the UK’s exit from the European Union.

After a second day of impassioned debate in the House of Commons, a total of 498 MPs voted to give a second reading to the short bill granting the government the power to invoke article 50, while 114 voted against.

A total of 47 Labour MPs voted against the Brexit bill, joining 50 SNP MPs and seven Liberal Democrats. Just one Conservative MP, Ken Clarke, joined them in the division lobbies, to applause from Labour rebels.

Rachael Maskell quit as shadow environment, food and rural affairs secretary, telling the Guardian: “I said I would first of all serve my constituents and that is the most important thing for me.”

Dawn Butler stepped down as shadow minister for diverse communities. She tweeted that it had “been an honour to serve in shadow cabinet doing a job I love. Can’t let down future generations voting against poor excuse of a bill”.

Corbyn thanked both MPs and described them as “great assets to the Labour party and to our movement”. The party leader will now have to carry out a fresh shadow cabinet reshuffle, just a few months after he filled the posts vacated by a wave of resignations over the summer.

Boris Johnson, the foreign secretary and the leading leave campaigner, issued a statement after the vote saying he had just voted in the Commons “for an absolutely momentous thing, which is to give our prime minister the right to trigger article 50 and begin the path out of the EU”.

He added: “But don’t forget we may be leaving the EU treaties but we are not leaving Europe. We will be making an amazingly positive contribution to our continent as we always have done and always will.”

Corbyn has struggled to contain the disquiet among Labour MPs about the risks of Brexit. The Labour leader has been clear since the morning after the referendum that Labour must respect the referendum result and allow article 50 to be triggered. But many of those, often inner city, MPs who represented remain-supporting areas felt they would be failing to represent their constituents if they backed the bill.

He will also have to decide how to discipline a number of other frontbenchers who voted against the bill, including three of his own whips – Thangam Debbonaire, Jeff Smith and Vicky Foxcroft. Labour sources said decisions on how to handle these cases would be made later.

Several remain-backing Conservatives also expressed their concerns about the government’s plans for Brexit during the two-day debate, with former chancellor George Osborne warning that May had decided not to make the economy the first priority as she opens negotiations.

But Downing Street bought off potential Tory rebels with the promise of a white paper on the government’s negotiating plans, which will be published on Thursday, and a vote at the end of the process, though Brexit secretary David Davis has stressed that does not mean parliament will be able to block Brexit.

Although remain-supporting Tories overwhelmingly voted in favour, some are still threatening to rebel when the Commons considers amendments to the bill next week, citing issues such as the rights of EU citizens to stay in the UK.

Earlier on Wednesday, Theresa May had told MPs at PMQs: “This House has a very simple decision to take. We gave the right of judgment on this matter to the British people, and they made their choice: they want to leave the EU. The question every member must ask themselves as they go through the lobby tonight is: do they trust the people?”

Liberal Democrat leader Tim Farron suffered a mini-rebellion of his own, with two of his party’s nine MPs, Norman Lamb and Greg Mulholland, choosing to abstain. After the debate, Farron said: “The Tories and Labour have failed future generations by supporting a hard Brexit. Labour’s leadership have waved the white flag. They are not an opposition, they are cheerleaders.”

The Brexit debate has amplified the divide between Labour’s metropolitan, liberal strongholds and its traditional heartlands in post-industrial areas of Britain, many of which voted strongly to leave. Other frontbenchers who voted against the party line, and whose futures are now in doubt, include Cambridge MP Daniel Zeichner and Tooting MP Rosena Allin-Khan.

In a statement after Wednesday’s resignations, Corbyn said: “MPs have a duty to represent their constituents as well as their party, and I understand the difficulties that MPs for constituencies which voted remain have in relation to the European Union withdrawal bill.”

Senior party sources suggested chief whip Nick Brown, a veteran of party battles, was advising Corbyn to be “flexible” in handling MPs from remain-leaning seats who felt they couldn’t back the bill.

Corbyn could suffer more resignations in the coming days. Clive Lewis, the shadow business secretary, has suggested he could yet vote against the third reading of the bill if Labour fails to have it amended. The vote on the third reading is expected to take place on next Wednesday, before debate passes to the House of Lords.

Rachael Maskell, who resigned from the shadow cabinet to defy the Labour whip to vote against triggering article 50. Photograph: Danny Lawson/PA

Labour sources said Lewis had been encouraged to step down this week, rather than prolong the agony for Corbyn. In total, including the three whips and those who had already resigned, more than sixteen frontbenchers defied the party line.

Ben Bradshaw, a Labour former minister, said the size of the Labour rebellion had exceeded expectations and some MPs had made their mind up in the chamber.

“It’s never an easy thing to do to vote against a three-line whip,” he said. “It is the first time I have voted against a three-line whip in nearly 20 years in the House. I think there will be more Labour MPs voting with us at third reading if, as we fear, the government does not accept any of our very reasonable amendments. I hope we can persuade more than a single moderate pro-European Conservative.”

He said there were discussions going on about trying to draft anamendment that would attract enough support to pass on securing a more meaningful vote at the end of the negotiating process.

Diane Abbott, Corbyn’s closest ally, did not vote for the bill but her office said she was ill.

Keir Starmer, the shadow Brexit secretary – who voted for the second reading, has sought to walk a difficult line between respecting the result of the referendum and continuing to represent the views of pro-remain Labour voters. In his London constituency, Holborn and St Pancras, 73.3% voted to remain.

Commenting on the second reading of the bill, a spokesperson for Corbyn said: “Labour MPs voted more than three to one in favour of triggering article 50. Now the battle of the week ahead is to shape Brexit negotiations to put jobs, living standards and accountability centre stage.

“Labour’s amendments are the real agenda. The challenge is for MPs of all parties to ensure the best deal for Britain, and that doesn’t mean giving Theresa May a free hand to turn Britain into a bargain basement tax haven.”